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Hello,

I'm interested in locating the MGN and LGN using segmentationThalamicNuclei, but there seems to be a mismatch between the location I obtain in the discrete segmentation and the underlying probability maps obtained by setting environment variable WRITE_POSTERIORS to 1. While the LGN segmentation (orange and dark blue below) has many voxels within the corresponding area of maximum probability (superimposed hot color scale thresholded at p>0.2 below), the MGN is almost absent from the discrete segmentation (or way too lateral/posterior/superior relative to its area of max probability to be seen in the screen shot below). Any reason why this could be happening? Is there anything I can do (parameters I can change) to fix this?

The defaut Freesurfer segmentation ("thalamus proper", shown in white below) is generally larger than the segmentation output by segmentThalamicNuclei, except in the area of the LGN, where the thalamic segmentation extends more laterally/inferiorly, as if it had been extended in order to include the LGN (although imperfectly). However, this does not seem to be happening for the MGN (which is my primary area of interest).

(Note that I'm using T1-weighted MPRAGE data at a resolution of 0.7 mm isotropic)